| Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-11-06 12:01 -0500 (Thu, 06 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4902 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4638 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1797/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RiboProfiling 1.40.0 (landing page) A. Popa
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
To the developers/maintainers of the RiboProfiling package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RiboProfiling.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: RiboProfiling |
| Version: 1.40.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data RiboProfiling |
| StartedAt: 2025-11-05 18:01:46 -0500 (Wed, 05 Nov 2025) |
| EndedAt: 2025-11-05 18:03:12 -0500 (Wed, 05 Nov 2025) |
| EllapsedTime: 86.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data RiboProfiling
###
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* checking for file ‘RiboProfiling/DESCRIPTION’ ... OK
* preparing ‘RiboProfiling’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘RiboProfiling.Rnw’ using knitr
2025-11-05 18:02:45.501 R[87670:638041388] XType: Using static font registry.
Quitting from RiboProfiling.Rnw:319-349 [CountReads]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! subscript contains invalid names
---
Backtrace:
x
1. +-RiboProfiling::countShiftReads(...)
2. +-exonGRanges[names(cdsPosTransc)]
3. \-exonGRanges[names(cdsPosTransc)]
4. +-methods::callNextMethod(x = x, i = i)
5. | \-base::eval(call, callEnv)
6. | \-base::eval(call, callEnv)
7. \-S4Vectors (local) .nextMethod(x = x, i = i)
8. \-S4Vectors:::subset_along_ROWS(x, i, drop = drop)
9. +-S4Vectors::extractROWS(x, i)
10. \-GenomicRanges (local) extractROWS(x, i)
11. \-IRanges (local) METHOD(x, i)
12. \-S4Vectors::normalizeSingleBracketSubscript(i, x, as.NSBS = TRUE)
13. +-S4Vectors::NSBS(...)
14. \-S4Vectors::NSBS(...)
15. \-S4Vectors:::.subscript_error("subscript contains invalid ", what)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'RiboProfiling.Rnw' failed with diagnostics:
subscript contains invalid names
--- failed re-building ‘RiboProfiling.Rnw’
SUMMARY: processing the following file failed:
‘RiboProfiling.Rnw’
Error: Vignette re-building failed.
Execution halted